Arm Of Chromosome Research Articles

Вариабельность признаков синдрома делеции 2q37 на примере клинических наблюдений

2q37 deletion syndrome is characterized by terminal deletions of the long arm of chromosome 2 and a variable clinical picture that includes type E brachydactyly, obesity, delayed motor and psychomotor development, congenital malformations of internal organs and the facial phenotype particular qualities. Authors present the two clinical case reports of patients with 2q37 deletions demonstrating different clinical manifestations. Proband 1 complained exclusively of brachydactyly while proband 2 had almost the full spectrum of clinical symptoms characterizing the syndrome. The Face2Gene AI-Powered Diagnosis & Care Management Tool suggested the correct diagnosis in both cases based on the features of the facial phenotype that in its turn became the key factors in choosing the tactics for further molecular genetic diagnostics. Conclusion: careful collection of anamnesis data, description of the facial phenotype and the use of artificial intelligence-based tools can become the key factors in choosing the tactics for the molecular genetic diagnostics available for practitioners of various specialties.

Molecular identification of a Pm4 allele conferring powdery mildew resistance in durum wheat DR88

BackgroundPowdery mildew, caused by Blumeria graminis f. sp. tritici (Bgt), is one of the most destructive wheat diseases worldwide. Durum wheat (Triticum turgidum L. var. durum Desf.) is a crucial gene donor for improving common wheat.ResultsIn this study, we investigated a durum wheat accession, DR88, which exhibits broad and high levels of resistance to powdery mildew. Using bulked segregant RNA-Seq (BSR-Seq), we identified a dominant gene, tentatively designated PmDR88, and localized it to 743–776 Mb interval on chromosome arm 2AL according to the reference genome of durum wheat cv. Svevo. Subsequently, PmDR88 was mapped in a genetic region of 3.9 cM flanked by the markers WGRE77410 and WGRC872 at genetic distances of 1.6 and 2.3 cM, respectively; it also co-segregated with JS717×JS718, the diagnostic marker for the Pm4 locus. Genotyping of a large population comprising 5,174 F2:3 families using JS717×JS718 confirmed that PmDR88 is located at the Pm4 locus on 2AL. Sequence alignment revealed that PmDR88 shares identical amino acid sequences with Pm4d, while qRT-PCR analysis suggested distinct expression patterns for PmDR88 compared with previously reported Pm4 alleles. Two complementary DNA markers, including the dominant co-segregating marker JS717×JS718 and a newly developed closely-linked co-dominant marker WGRE77410, were confirmed to be available for efficiently transferring PmDR88 into the tested wheat backgrounds by marker-assisted selection (MAS) strategy.ConclusionsPmDR88 was mapped in the Pm4 locus. Despite sharing identical amino acid sequences with Pm4d, PmDR88 exhibits distinct expression patterns. Moreover, DR88 shows broad and high levels of resistance to powdery mildew. Two complementary DNA markers were identified for MAS breeding. The molecular identification of PmDR88 will facilitate transfer of this Pm4 allele into susceptible cultivars for resistance improvement or into resistant cultivars for resistance-enhanced pyramiding breeding.

A detailed karyological investigation of three endemic Cobitis L. 1758 species (Teleostei, Cobitidae) in Anatolia, Türkiye.

Comparative cytogenetics is a vital approach for diagnosing chromosome abnormalities and identifying species-specific patterns. In this study, chromosomal analysis of three Anatolian endemic Cobitis species was performed. Conventional cytogenetic techniques such as Giemsa staining, C-banding and Ag-NOR staining were applied, followed by measurements of chromosome arm lengths including analysis of the measured data. The diploid chromosome number, 2n = 50, was determined for all three species. The karyotype formulas were as follows: four pairs of metacentric, five pairs of submetacentric, and 16 pairs of subtelo-telocentric chromosomes in Cobitis bilseli; 11 pairs of metacentric, seven pairs of submetacentric, and seven pairs of subtelo-telocentric chromosomes in C. fahireae; and four pairs of metacentric, four pairs of submetacentric, and 17 pairs of subtelo-telocentric chromosomes in C. turcica. Dark C-bands were observed on the pericentromeres of nearly all chromosomes in C. bilseli and C turcica, whereas light C-bands appeared on the pericentromeres of some chromosomes in C. fahireae. Silver-stained metaphases revealed signals on the short arm of a submetacentric chromosome pair in C. fahireae (each homologous chromosome carries one signal), while in C. bilseli and C. turcica, Ag-NOR signals were detected on the long arm of a single metacentric chromosome (only one homologous chromosome carries the signal, and the signal-carrying chromosome is the largest chromosome in the karyotype). This study provides new cytogenetic data consistent with the phylogenetic distances between the studied species, indicating pericentric inversions and/or translocations that govern the formation of Cobitis karyotypes.

Two major-effect loci influence interspecific mating in females of the sibling species, Drosophila simulans and D. sechellia.

Secondary contact between incompletely isolated species can produce a wide variety of outcomes. The vinegar flies Drosophila simulans and D. sechellia diverged on islands in the Indian Ocean and are currently separated by partial pre- and postzygotic barriers. The recent discovery of hybridization between D. simulans and D. sechellia in the wild presents an opportunity to monitor the prevalence of alleles that influence hybridization between these sibling species. We therefore sought to identify those loci in females that affect interspecific mating, and we adapted a two-choice assay to capture female mate choice and female attractiveness simultaneously. We used shotgun sequencing to genotype female progeny of reciprocal F1 backcrosses at high resolution and performed QTL analysis. We found two major-effect QTL in both backcrosses, one on either arm of the third chromosome that each account for 32-37% of the difference in phenotype between species. The QTL of both backcrosses overlap and may each be alternate alleles of the same locus. Genotypes at these two loci followed an assortative mating pattern with D. simulans males but not D. sechellia males, which mated most frequently with females that were hybrid at both loci. These data reveal how different allele combinations at two major loci may promote isolation and hybridization in the same species pair. Identification of these QTL is an important step towards understanding how the genetic architecture of mate selection may shape the outcome of secondary contact.

Genome editing with the HDR-enhancing DNA-PKcs inhibitor AZD7648 causes large-scale genomic alterations.

The DNA-PKcs inhibitor AZD7648 enhances CRISPR-Cas9-directed homology-directed repair efficiencies, with potential for clinical utility, but its possible on-target consequences are unknown. We found that genome editing with AZD7648 causes frequent kilobase-scale and megabase-scale deletions, chromosome arm loss and translocations. These large-scale chromosomal alterations evade detection through typical genome editing assays, prompting caution in deploying AZD7648 and reinforcing the need to investigate multiple types of potential editing outcomes.

Rare Maternal Structural Mosaicism as a Familial Cause of 18p Deletion Syndrome: Cytogenetics Mechanisms and Phenotypic Variability

The chromosome 18p deletion (18p-) syndrome or monosomy of 18p is a rare chromosome abnormality, considered a contiguous gene deletion syndrome resulting from the deletion of a portion or most of the whole short arm of chromosome 18. Therefore, it can present a spectrum of phenotypes associated with different prognostic outcomes. Understanding the clinical variability of this condition is important once the fertility is preserved, impacting genetic counseling and reproductive outcomes. The aim of this article is to report a case of familial 18p deletion syndrome and its striking phenotypic variability within the same family. A male stillborn presenting alobar holoprosencephaly and his mother who presented with a single central incisor came to our attention for genetic investigation. Karyotype analysis and Fluorescent In Situ Hybridization (FISH) from a cordocentesis blood sample of the male stillborn was performed. Parents’ cytogenetic analyses were obtained through peripheral blood cultures. Chromosomes were analyzed after GTG banding. FISH technique was carried out on both the proband's and maternal samples using WCP18 (whole chromosome 18) specific probes, according to the manufacturer's protocols. The stillborn karyotype and FISH analysis revealed a deletion characterized by 46, XY del(18)(p11.1→pter).ish del(18)(p11.1→pter)(wcp18-). His mother showed the same deletion in 45% of the analyzed cells revealing a rare structural mosaicism. The striking phenotypic variability encountered in this family could be attributed to a genetic combination of the deleted segment in the proband; and the presence of a mosaic normal karyotype may very well attenuate the mother’s phenotypic presentation. The origin of an abnormally structural chromosome in mosaic possibly originated from a post-zygotic cell division event during the embryonic development of the mother. The consequences on the family offsprings of such rare cytogenetic event impacts greatly the family genetic counseling

Generation of Monosomy 21q Human iPS Cells by CRISPR/Cas9-Mediated Interstitial Megabase Deletion.

Missing an entire chromosome or chromosome arm in normal diploid cells has a deleterious impact on cell viability, which may contribute to the development of specific birth defects. Nevertheless, the effects of chromosome loss in human cells have remained unexplored due to the lack of suitable model systems. Here, we developed an efficient, selection-free approach to generate partial monosomy in human induced pluripotent stem cells (iPSCs). The introduction of Cas9 proteins and a pair of gRNAs induces over megabase-sized interstitial chromosomal deletions. Using human chromosome 21 (HSA21) as a model, partial monosomy 21q (PM21q) iPSC lines with deletions ranging from 4.5 to 27.9 Mb were isolated. A 33.6 Mb deletion, encompassing all protein-coding genes on 21q, was also achieved, establishing the first 21q monosomy human iPSC line. Transcriptome and proteome analyses revealed that the abundances of mRNA and protein encoded by the majority of genes in the monosomic regions are half of the diploid expression level, indicating an absence of dosage compensation. The ability to generate customized partial monosomy cell lines on an isogenic, karyotypically normal background should facilitate the gain of novel insights into the impact of chromosome loss on cellular fitness.

The histone demethylase Kdm5 controls Hid-induced cell death in Drosophila

We conducted an EMS mutagenesis screen on chromosome arm 2L to identify recessive suppressors of GMR-hid-induced apoptosis in the Drosophila eye. Through this screen, we recovered three alleles of the lysine demethylase gene Kdm5. Kdm5, a member of the JmjC-domain-containing protein family, possesses histone demethylase activity towards H3K4me3. Our data suggest that Kdm5 specifically regulates Hid-induced cell death during development, as we did not observe control of Reaper- or Grim-induced cell death by Kdm5. Interestingly, GMR-hid-induced apoptosis is suppressed independently of Kdm5’s demethylase activity. Our findings indicate that Rbf and dMyc are necessary for Kdm5 mosaics to suppress GMR-hid-induced cell death. Moreover, Kdm5 mosaics failed to suppress apoptosis induced by a mutant form of Hid that is resistant to inhibition by Erk-type MAPK activity. Additionally, Kdm5 dominantly enhances the wing phenotype of an activated MAPK mutant. These results collectively suggest that Kdm5 controls Hid-induced apoptosis by regulating the Rbf, dMyc, and MAPK pathways.

Identification of a novel hybrid sterility locus S67 between temperate japonica subgroup and basmati subgroup in Oryza sativa L

Asian cultivated rice (Oryza sativa L.) is the most important cultivated species in the AA genome species of the genus Oryza. basmati is a special and famous subgroup in Asian cultivated rice, and temperate japonica is one of the most important cultivated subgroup, too. However, hybrid sterility hinders the introgression of favorable traits and the utilization of hybrid vigour between the two subgroups. The genetic basis of intraspecific hybrid sterility between temperate japonica and basmati remained elusive. In this study, a novel hybrid sterility locus S67 was identified, which caused hybrid male sterility in hybrids between the temperate japonica rice variety Dianjingyou 1 (DJY1) and the basmati rice variety Dom-sufid. Initial mapping with BC1F1, BC4F1, BC4F2 populations and DNA markers located S67 between RM5362 and K1-40.6 on the long arm of chromosome 1. Genetic analysis confirmed that S67 caused a transmission advantage for the temperate japonica rice S67-te allele in the hybrid offsprings. This result not only fills the gap in the research on hybrid sterility between basmati and temperate japonica, but also lays a good foundation for the systematic study of the genetic nature of hybrid sterility between basmati and other subgroups, as well as the full exploration and utilization of this subgroup through the creation of wide or specific compatibility lines to overcome hybrid sterility. In addition, this result can also help us broaden our understanding of genetic differentiation within Asian cultivated rice and hybrid sterility between inter-subgroups.

Acentric chromosome congression and alignment on the metaphase plate via kinetochore-independent forces in Drosophila.

Chromosome congression and alignment on the metaphase plate involves lateral and microtubule plus-end interactions with the kinetochore. Here we take advantage of our ability to efficiently generate a GFP-marked acentric X chromosome fragment in Drosophila neuroblasts to identify forces acting on chromosome arms that drive congression and alignment. We find acentrics efficiently congress and align on the metaphase plate, often more rapidly than kinetochore-bearing chromosomes. Unlike intact chromosomes, the paired sister acentrics oscillate as they move to and reside on the metaphase plate in a plane distinct and significantly further from the main mass of intact chromosomes. Consequently, at anaphase onset acentrics are oriented either parallel or perpendicular to the spindle. Parallel-oriented sisters separate by sliding while those oriented perpendicularly separate via unzipping. This oscillation, together with the fact that in the presence of spindles with disrupted interpolar microtubules acentrics are rapidly shunted away from the poles, indicates that distributed plus-end directed forces are primarily responsible for acentric migration. This conclusion is supported by the observation that reduction of EB1 preferentially disrupts acentric alignment. Taken together these studies suggest that plus-end forces mediated by the outer interpolar microtubules contribute significantly to acentric congression and alignment. Surprisingly, we observe disrupted telomere pairing and alignment of sister acentrics indicating that the kinetochore is required to ensure proper gene-to-gene alignment of sister chromatids. Finally, we demonstrate that like mammalian cells, the Drosophila congressed chromosomes on occasion exhibit a toroid configuration.

Genetic Analysis of Stripe Rust Resistance in the Chinese Wheat Cultivar Luomai 163.

Stripe or yellow rust (YR) caused by Puccinia striiformis tritici (Pst) is an important foliar disease affecting wheat production globally. Resistant varieties are the most economically and environmentally effective way to manage this disease. The common winter wheat (Triticum aestivum L.) cultivar Luomai 163 exhibited resistance to the Pst races CYR32 and CYR33 at the seedling stage and showed a high level of adult plant resistance in the field. To understand the genetic basis of YR resistance in this cultivar, 142 F5 recombinant inbred lines (RILs) derived from cross Apav#1 × LM163 and both parents were genotyped with the 16K SNP array and bulked segregant analysis sequencing. The analysis detected a major gene, YrLM163, at the seedling stage associated with the 1BL.1RS translocation. Additionally, three genes for resistance at the adult plant stage were detected on chromosome arms 1BL (Lr46/Yr29/Pm39/Sr58), 6BS, and 6BL in Luomai 163, whereas Apav#1 contributed resistance at a quantitative trait locus (QTL) on 2BL. These QTL explained YR disease severity variations ranging from 6.9 to 54.8%. The kompetitive allele-specific PCR (KASP) markers KASP-2BL, KASP-6BS, and KASP-6BL for the three novel loci QYr.hzau-2BL, QYr.hzau-6BS, and QYr.hzau-6BL were developed and validated. QYr.hzau-1BL, QYr.hzau-2BL, and QYr.hzau-6BS showed varying degrees of resistance to YR when present individually or in combination based on genotype and phenotype analysis of a panel of 570 wheat accessions. Six RILs combining resistance alleles of all QTL, showing higher resistance to YR in the field than Luomai 163 with disease severities of 10.7 to 16.0%, are important germplasm resources for breeding programs to develop YR-resistant wheat varieties with good agronomic traits.

Imaging of cystic fibrosis manifestations in the abdomen.

Cystic fibrosis is a common inherited autosomal recessive disease affecting 35,000 persons in the United States. It is caused by mutations of the cystic fibrosis transmembrane regulator (CFTR) gene, located on the long arm of chromosome 7.This protein carries chlorine in the membranes of epithelial cells of exocrine glands. Mutations in the CFTR gene results in production of abnormally viscous mucus. Although it primarily affects the lungs, cystic fibrosis is a multisystem disease with involvement of extra thoracic organs including the liver, pancreas, kidneys and digestive tract.With advances in the management of cystic fibrosis resulting in improved life expectancy, cystic fibrosis patients are surviving into adulthood and extrapulmonary disease has become more commonplace. It is essential that radiologists are aware of the spectrum of potential manifestations of cystic fibrosis to allow accurate diagnosis.The purpose of this manuscript is to provide an overview of the pathophysiology and imaging findings of abdominal entities unique to patients with cystic fibrosis. We will present a wide spectrum of renal, pancreatic, gastrointestinal, hepatobiliary and post-transplant cases describing the typical findings that will assist radiologists in providing a timely diagnosis for patients with cystic fibrosis.

EPCO-12. MENINGIOMA COPY NUMBER ANALYSIS IDENTIFIES OPTIMIZED SIZE THRESHOLDS AND CO-OCCURRENCE MODELS FOR INDIVIDUALIZED RISK-STRATIFICATION

Abstract Arm-level copy number alterations (CNAs) are common in meningiomas and are useful for risk-stratification, but there is no consensus regarding the optimal size threshold to define CNAs for prognostic models. Moreover, the prognostic importance of co-occurring CNA pairs and overall CNA burden in meningiomas remains incompletely understood. To address this, CNAs were analyzed in 691 retrospective meningiomas with clinical data and DNA methylation profiles from 3 international institutions. Arm-level CNAs were defined from DNA methylation profiles using iterative size thresholds ranging from 1-99% of each chromosome arm. The area under the curve (AUC) for 5-year local freedom from recurrence (LFFR) or overall survival (OS) was calculated using CNAs across size thresholds, and AUC standard deviation across thresholds was used as a measure of size-dependence. LASSO and Elastic Net Cox regressions were used to generate multi-CNA models for LFFR or OS and to identify prognostic co-occurring CNA pairs. These analyses identified 13 size-dependent prognostic CNAs in meningiomas, including loss of 1p, 3q, 4p, 4q, 6p, 6q, 9p, 10q, 12q, 14q,18q, and 22q, and gain of 1q. Regression models restricted to size-dependent CNAs improved risk stratification within strata of previously published models (Integrated score, Integrated grade), and identified prognostic CNAs not included in previous models, such as 1q gain, 7p loss, and 12q loss. Ontology analysis of genes in focal prognostic CNAs identified dysregulated STAT signaling and decreased expression of interferon-related genes from matched paired RNA sequencing. Models of size-dependent, prognostic, co-occurring CNA pairs identified 1p/22q codeletion, 1q gain/22q loss, and 9p/18q codeletion as significant predictors of LFFR. Increased CNA burden correlated with higher tumor grade and was significantly associated with worse LFFR and OS. In summary, chromosome-specific size thresholds identify prognostic arm-level CNAs and co-occurring CNA pairs in meningiomas. Thus, granular copy number analysis may improve risk stratification models for meningioma.

PATH-59. HISTOLOGIC CORRELATES FOR MOLECULAR FEATURES IN MENINGIOMAS

Abstract Histologic findings are the primary determinant of meningioma prognosis and post-operative management. However, the association of specific pathologic features with molecular alterations has not yet been comprehensively investigated. Here we utilized a large dataset of well-characterized meningiomas to identify correlates between clinically relevant histological and molecular features. Detailed histologic information was collected for 809 resected meningiomas, including cases with DNA methylation (n=380), copy number array (n=252), next-generation sequencing (n=52), RNA risk score (n=394), and/or TERT promoter profiling (n=238). Analyses were conducted on prognostic pathologic features, including WHO Grade, Ki-67, mitotic index (MI), brain invasion, and atypical histologic findings (necrosis, hypercellularity, prominent nucleoli, sheeting, and small cells). Correlation with molecular variables was performed using Fisher’s Exact Tests, including DNA methylation subgroup, RNA risk score, CNV profiles, and TERT promoter mutations. All statistics were corrected for multiple hypothesis testing. Nearly 65% of meningiomas exhibited at least one atypical histologic feature. Among said features, Ki-67/MI, WHO Grade, sheeting, and necrosis were associated with recurrent lesions and known clinical features of aggressive meningiomas. Several histologic features, including hypercellularity, elevated Ki-67/mitotic index, and WHO grade, also correlated with DNA methylation and RNA risk groups. Several chromosomal arm events were related to specific pathologic features (prominent nucleoli, Ki-67, MI, and grade), including chromosomes 1, 4, 10, 14, and 18. Our analysis highlights the continued value in screening for histologic markers of aggressive behavior in meningiomas, as they correlate with the presence of high-risk molecular features and may serve as proxy markers when advanced molecular testing is not available.

Clinical phenotype and genetic analysis of a child with partial duplication of 10q and a literature review

To explore the clinical phenotype and pathogenesis of a child with partial duplication in the long arm of chromosome 10 (10q), and conduct a review of relevant literature. A child presented at Lianyungang Maternal and Child Health Care Hospital in April 2018 for growth retardation, intellectual disability, and autism spectrum disorder (ASD) was selected as the study subject. Peripheral blood samples were collected from the child and his parents for G-banded chromosomal karyotyping analysis. Genomic DNA was also extracted for chromosomal microarray analysis (CMA). The clinical phenotype and relevant genes were searched in the Online Mendelian Inheritance in Man (OMIM) and the UK Database of Genomic Variation and Phenotype in Humans using Ensembl Resources (DECIPHER). The pathogenicity of chromosomal variation was analyzed based on guidelines from the American College of Medical Genetics and Genomics (ACMG). Relevant literature was searched from the CNKI, Wanfang Data, and PubMed databases by using keywords such as "10q" "duplication" and "trisomy", with the time set as from the establishment of database to December 1, 2023. This study has been approved by the Medical Ethics Committee of the Lianyungang Maternal and Child Health Care Hospital (No. XM2023030). The clinical phenotype of child had included growth retardation, intellectual disability, and ASD. G-banded chromosomal analysis suggested that the child has a karyotype of 46,XY,dup(10)(q23.31q24.33), whilst both of his parents were normal. CMA analysis of the child revealed that the child was arr[19]10q23.31q24.33(87603382_104948862)×3, with a 17.34 Mb duplication in the 10q23.31q24.33 region. Search of the OMIM database suggested that the duplicated segment has contained 171 genes associated with various diseases, and search of the DECIPHER database has identified cases with overlapping with the duplication. A search of the PubMed database has identified 2 publications involving 2 patients with chromosomal duplications overlapping the 10q23.31q24.33 region with a segment length of > 10 Mb. The 2 patients had mainly manifested growth retardation, intellectual disability, ASD, and facial and limb malformations. The main pathogenic genes had included PTEN, WNT8B, LZTS2, NFKB2, PAX2, KIF11, FRA10AC1, and CNNM2. No similar case was retrieved from the CNKI and Wanfang Data databases. The partial 10q duplication as a novel CNV involving genes such as PTEN and WNT8B probably underlay the growth retardation, intellectual disability and ASD in child 1 . This study has enriched the genotype-phenotype spectrum of patients with partial 10q23.31q24.33 duplications.

Characterization of a new barley greenbug resistance gene Rsg4 in the Chinese landrace CI 2458.

Barley (Hordeum vulgare) is a climate-resilient crop widely cultivated in both highly productive and suboptimal agricultural systems, and its ability to adapt to multiple biotic and abiotic stresses has contributed significantly to food security. Greenbug is a destructive insect pest for global barley production, and new greenbug resistance genes are needed to overcome the challenges posed by diverse greenbug biotypes in fields. CI 2458 is a Chinese landrace exhibiting a unique resistance profile to a set of 14 greenbug biotypes, which suggests the presence of a new greenbug resistance gene in CI 2458. A recombinant inbred line population from the cross Weskan × CI 2458 was developed, evaluated for responses to greenbug biotype F, and genotyped using single nucleotide polymorphism (SNP) markers generated by genotyping-by-sequencing. Linkage analysis revealed a single gene, designated Rsg4, conditioning greenbug resistance in CI 2458. Rsg4 was delimited to a 1.14 Mb interval between SNP markers S3H_666512114 and S3H_667651446 in the terminal region of chromosome arm 3HL, with genetic distances of 1.2 cM proximal to S3H_667651446 and 1.1 cM distal to S3H_666512114. Allelism tests confirmed that Rsg4 is a new greenbug resistance gene independent of Rsg1 and Rsg3, which reside in the same chromosome arm. Rsg4 differs from Rsg1 alleles and Rsg3 in its resistance to greenbug biotype TX1, one of the most widely virulent biotypes. The introgression of Rsg4 into locally adapted barley cultivars is of agronomic importance, and kompetitive allele-specific polymerase chain reaction (KASP) markers flanking Rsg4, KASP-Rsg336-1 and KASP-Rsg336-2, enable rapid pyramiding of Rsg4 with other resistance genes to develop durable greenbug-resistant cultivars.

Evolutionary history written in tandem arrays – satellite repeats in the Lagoseris lineage of Crepis sensu lato (Asteraceae)

Abstract Satellite DNA families are excellent markers in evolutionary studies of plant karyotypes. Together with phylogenetic background, they can provide additonal information on different scenarios accompanying the speciation and diversification of related species. The Lagoseris lineage of Crepis sensu lato constitutes an interesting model in such studies, mainly due to: (i) the presence of large chromosomes; (ii) several base chromosome numbers; and (iii) variation in genome sizes. We aimed to characterize the satellite families and compare their genomic and chromosomal organization to better understand the evolutionary pathways that shaped the genomes of the Lagoseris lineage. Eight different families of satellite repeats were identified in Crepis palaestina based on RepeatExplorer raw Illumina read analyses. Most of these satellites were present in five species studied from the Lagoseris lineage and organized in tandem arrays. If the particular repeat was present in the genome of the related species, its genomic organization showed similarity to the one observed in C. palaestina. This similar genomic organization was not often reflected at the chromosomal level, where many distinct distribution patterns were shown, from several major loci to numerous minor ones spread throughout the chromosomal arms. The evolution of satellite repeats is discussed in phylogenetic context.

LncRNA HAGLROS: A Vital Oncogenic Propellant in Various Human Cancers.

HAGLR Opposite Strand lncRNA (HAGLROS) is a long non-coding RNA (lncRNA) located on the long arm of human chromosome 2 at locus 2q31.1. Emerging evidence highlights HAGLROS as a pivotal player in human cancers, characterized by its significant upregulation across multiple malignancies where it functions as an oncogenic driver. Its aberrant expression is closely linked to the initiation and progression of 13 distinct cancer types, notably correlating with adverse clinical outcomes and reduced overall survival rates in 9 of these cancer types. Mechanistically, HAGLROS is under the regulatory influence of the transcription factor STAT3, exerts competitive binding to 9 miRNAs, activates 5 signaling pathways pivotal for cancer cell proliferation and metastasis, as well as intricately modulates gene expression profiles. Given its multifaceted roles, HAGLROS emerges as a promising candidate for cancer diagnostics and prognostics. Moreover, its potential as a therapeutic target holds considerable promise for novel treatment strategies in oncology. This review synthesizes current research on HAGLROS, covering its expression patterns, biological roles, and clinical significance in cancer. By shedding light on these aspects, this review aims to contribute new perspectives that advance our understanding of cancer biology, enhance diagnostic accuracy, refine prognostic assessments, and pave the way for targeted therapeutic interventions.

Evaluation of durum and hard red spring wheat panels for sensitivity to necrotrophic effectors produced by Parastagonospora nodorum.

Septoria nodorum blotch is an important disease of both durum and hard red spring wheat (HRSW) worldwide. The disease is caused by the necrotrophic fungal pathogen Parastagonospora nodorum when compatible gene-for-gene interactions occur between pathogen-produced necrotrophic effectors (NEs) and corresponding host sensitivity genes. To date, nine sensitivity gene-NE interactions have been identified, but there is little information available regarding their overall frequency in durum and HRSW. Here, we infiltrated a global HRSW panel (HRSWP) and the Global Durum Panel (GDP) with P. nodorum NEs SnToxA, SnTox1, SnTox267, SnTox3, and SnTox5. Frequencies of sensitivity to SnTox1 and SnTox5 were higher in durum compared to HRSW and vice versa for SnTox267 and SnTox3. Strong associations for the known sensitivity loci Tsn1, Snn1, Snn2, Snn3, Snn5, and Snn7 along with potentially novel sensitivity loci on chromosome arms 7DS and 3BL associated with SnToxA and SnTox267, respectively, were identified in the HRSWP. In the GDP, Snn1, Snn3, and Snn5 were identified along with novel loci associated with sensitivity to SnTox267 on chromosome arms 2AS, 2AL, and 6AS and with SnTox5 sensitivity on 2BS and 7BL. These results reveal additional NE sensitivity loci beyond those previously described demonstrating a higher level of genetic complexity of the wheat-P. nodorum system than previously thought. Knowledge regarding the prevalence and genomic locations of SNB susceptibility genes in HRSW and durum will prove useful for developing efficient breeding strategies and improving varieties for SNB resistance.

The kinase ATR controls meiotic crossover distribution at the genome scale in Arabidopsis

Abstract Meiotic crossover, i.e. the reciprocal exchange of chromosome fragments during meiosis, is a key driver of genetic diversity. Crossover is initiated by the formation of programmed DNA double-strand breaks (DSBs). While the role of ATAXIA-TELANGIECTASIA AND RAD3-RELATED (ATR) kinase in DNA damage signaling is well-known, its impact on crossover formation remains understudied. Here, using measurements of recombination at chromosomal intervals and genome-wide crossover mapping, we showed that ATR inactivation in Arabidopsis (Arabidopsis thaliana) leads to dramatic crossover redistribution, with an increase in crossover frequency in chromosome arms and a decrease in pericentromeres. These global changes in crossover placement were not caused by alterations in DSB numbers, which we demonstrated by analyzing phosphorylated H2A.X foci in zygonema. Using the seed-typing technique, we found that hotspot usage remains mainly unchanged in atr mutants compared with wild-type individuals. Moreover, atr showed no change in the number of crossovers caused by two independent pathways, which implies no effect on crossover pathway choice. Analyses of genetic interaction indicate that while the effects of atr are independent of MMS AND UV SENSITIVE81 (MUS81), ZIPPER1 (ZYP1), FANCONI ANEMIA COMPLEMENTATION GROUP M (FANCM), and D2 (FANCD2), the underlying mechanism may be similar between ATR and FANCD2. This study extends our understanding of ATR's role in meiosis, uncovering functions in regulating crossover distribution.